2.1. Binding Interactions
The binding of molecules to each other involves direct partner specificity, interaction and stability. The strength of the interaction is determined by the number of atomic bonds that are made and their overall length and strength. In general, bonds between catalytic biomolecules must be reversible because binding partners must be recycled. For example, in enzyme-substrate recognition, binding constants are low so that multiple rapid reactions can occur. Similarly, binding initiation interactions between promoter DNA and RNA polymerase also require less than maximal affinity and stability otherwise the RNA polymerase enzyme is unable to migrate from the promoter and is transcriptionally inactive. Thus, bonds between biological molecules are frequently not of the highest affinity and stability possible although binding reactions of structural and surface components that involve permanent cell-cell interactions and anchorage functions may be very stable with high affinity between the binding partners.
Binding can be accomplished by charge attraction between surfaces and/or by pairing complementary three dimensional molecular surfaces or structures, e.g. a protruding surface fitting into a cavity. The tertiary structure of the protrusion or cavity is the result of flexible polypeptide chains forming shapes that are determined by weak chemical bonds. Thus the amino acid sequence as the primary structure of a peptide provides the chemical subgroups that are aligned in proper position to effectuate proper interactions by the secondary and tertiary structure of the peptide. The types of weak bonds involved in tertiary structure include van der Waals bonds, hydrophobic bonds, hydrogen bonds and ionic bonds. Just as these bonds are involved in intramolecular structure, they can also be involved in intermolecular binding between macromolecules. Thus, intermolecular binding is accomplished by electrostatic bonds, hydrogen bonds, Van der Waals bonds, etc., as well as by combinations thereof. It is difficult to predict which amino acids in a region of a protein structure are responsible for what function, even with the aid of a known tertiary structure. It becomes even more difficult to predict the effect of specified amino acid changes. Predictions of important interacting sequences based on similarities of primary sequence can be incorrect for failure to recognize sequence similarity arising from a common genetic origin rather than from protein design and function constraints. See Subbiah, J. Mol. Biol. 206: 689 (1989). At this point in time it is not only impossible to predict what amino acid changes within a peptide will result in a new or altered protein function, it is also impossible to predict what sequence of amino acids will produce a peptide of given function. Thus, the analysis of known interactions at the molecular and atomic level is completely unsuitable for developing wholly new interactions, especially those that might not occur in nature where macromolecular interactions are limited to the constraints imposed by the aqueous environment within cells and the subsequent requirements of biological and biochemical interactions.
In contrast to the prior art which has not solved the difficulties of developing totally novel binding specificities, the present invention provides a method for producing polypeptides or proteins having a desired binding specificity similar to naturally occurring binding proteins which does not require detailed information with regard to either the specific amino acid sequence or secondary structure of the naturally occurring binding protein. In addition, the method provides a process to generate and identify new peptide compositions having new binding interactions that are not limited to natural interactions or constrained by the evolutionary process.